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Fluorescence microscopy through scattering media with robust matrix factorization

Cell Reports Methods 2025年第5期5卷 101031页

作者： Gao, Zijun Ling, Zhi Liu, Wenhao Han, Keyi Zhang, Hongmanlin Hua, Xuanwen Botchwey, Edward A. Jia, Shu Laboratory for Systems Biophotonics Georgia Institute of Technology Atlanta 30332 GA United States Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta 30332 GA United States Parker H. Petit Institute for Bioengineering and Biosciences Georgia Institute of Technology Atlanta 30332 GA United States School of Materials Science and Engineering Georgia Institute of Technology Atlanta 30332 GA United States George W. Woodruff School of Mechanical Engineering Georgia Institute of Technology Atlanta 30332 GA United States

Biological tissues, as natural scattering media, inherently disrupt structural information, presenting significant challenges for optical imaging. Complex light propagation through tissue severely degrades image quality, limiting conventional fluorescence imaging techniques to superficial depths. Extracting meaningful information from random speckle patterns is, therefore, critical for deeper tissue imaging. In this study, we present RNP (robust non-negative principal matrix factorization), an approach that enables fluorescence microscopy under diverse scattering conditions. By integrating robust feature extraction with non-negativity constraints, RNP effectively addresses challenges posed by non-sparse signals and background interference in scattering tissue environments. The framework operates on a standard epi-fluorescence platform, eliminating the need for complex instrumentation or precise alignment. The results from imaging scattered cells and tissues demonstrate substantial improvements in robustness, field of view, depth of field, and image clarity. We anticipate that RNP will become a valuable tool for overcoming scattering challenges in fluorescence microscopy and driving advancements in biomedical research. © 2025 The Author(s)

关键词： CP: Imaging CP: Systems biology fluorescence microscopy non-invasive imaging scattering imaging tissue imaging

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Design of flow channel with surface electrodes to detect dielectrophoretic movement of floating myoblast 23

Design of flow channel with surface electrodes to detect die...

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23rd World Multi-Conference on Systemics, Cybernetics and Informatics, WMSCI 2019

作者： Hashimoto, Shigehiro Hasegawa, Daisuke Takahashi, Yusuke Matsuzawa, Ryota Biomedical Engineering Department of Mechanical Engineering Kogakuin University Tokyo163-8677 Japan

ISBN: (纸本)9781950492206

A micro flow channel with the surface electrodes has been designed to detect the dielectrophoretic movement of a biological cell in vitro. A pair of asymmetric surface electrodes of titanium (thickness of 200 nm) were incorporated in the flow channel by the photolithography technique: a triangular electrode with the tip angle of 0.35 rad, and a rectangular electrode of the flat edge as reference. The rectangular cyclic alternating electric current was introduced between the surface electrodes. The suspension of C2C12 (mouse myoblast cell line) was injected into the flow channel, and the flow rate was controlled by the pressure head between the inlet and the outlet. The selected system design (the shape of the electrode, electric rectangular alternating current wave (±7.5 mA, 0.3 μs of period), and the flow velocity of 0.3 mm/s) is able to detect dielectrophoretic movement of floating C2C12. © WMSCI 2019 - 23rd World Multi-Conference on Systemics, Cybernetics and Informatics, Proceedings. All rights reserved.

关键词： Electrophoresis

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Response of unsteady thermocapillary convection to local heating at specific depths in a thin liquid film

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Chemical engineering Science 2025年 314卷

作者： Kudo, Masaki Igarashi, Keita Mechanical Systems Engineering Program Monozukuri Engineering Department Tokyo Metropolitan College of Industrial Technology 10-40 Higashi-oi 1-chome Tokyo Shinagawa City140-0011 Japan

A hydrothermal wave (HTW) refers to a flow pattern that arises during unsteady thermocapillary convection, negatively impacting the purity of single crystals during zone melting. This study utilized active control through localized heating to reduce HTW amplitude, akin to noise cancellation. The effectiveness of this method was evaluated both experimentally and numerically by adjusting the heating depth in a thin liquid film. Silicone oil served as the test fluid, and the liquid film was rectangular in shape. In the case of linear time-periodic heating, a line-shaped heater applied a constant maximum heat input, synchronized with the HTW's period. Experimental results indicated that HTW amplitude significantly depends on the heating depth of the liquid film. Downstream of the HTW, temperature amplitude could be reduced by up to 60%, whereas upstream, it could be amplified. In numerical simulations, HTW reduction and amplification were linked to substantial changes in the streamwise temperature gradient on the free surface, rather than to local cancellation of the temperature disturbance. Unlike the results from single-pulse heating control, the amplitude ratio showed a strong dependence on whether the heat input significantly affected the streamwise thermal and flow fields. © 2025 Elsevier Ltd

关键词： Liquid films

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mechanical Characterization of Biostable Dental Restoratives and Adhesives

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Dental Materials 2025年 41卷 e36-e36页

作者： Gouveia, Z Finer, Y Santerre, P Faculty of Dentistry University of Toronto Toronto Canada Institute of Biomedical Engineering University of Toronto Toronto Canada Translational Biology and Engineering Program University of Toronto Toronto Canada Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Canada

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Effect of Couette type of shear stress field with axial shear slope on deformation and migration of cell: Comparison between C2C12 and HUVEC 23

Effect of Couette type of shear stress field with axial shea...

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23rd World Multi-Conference on Systemics, Cybernetics and Informatics, WMSCI 2019

作者： Hashimoto, Shigehiro Sugimoto, Hiromi Hino, Haruka Biomedical Engineering Department of Mechanical Engineering Kogakuin University Tokyo163-8677 Japan

ISBN: (纸本)9781950492206

A shear flow device contained in the microscope incubator has newly been designed to study the effect of the shear stress field on the biological cell in vitro. The culture medium was sandwiched with a constant gap between a lower stationary culture plate and an upper rotating parallel plate to make a Couette type of shear field with the perpendicular shear slope. The wall shear stress (τ) on the lower culture disk was controlled by the rotating speed of the upper disk. The shear stress τ increases in proportion to the distance from the axis of rotation. After cultivation for 24 hours for adhesion of cells on the lower plate without flow, τ © WMSCI 2019 - 23rd World Multi-Conference on Systemics, Cybernetics and Informatics, Proceedings. All rights reserved.

关键词： Shear stress

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Risk factors for bone cement dislodgement following balloon kyphoplasty for osteoporotic vertebral compression fracture

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Neurochirurgie 2024年第4期70卷 101559-101559页

作者： Chang, Kai-Chieh Huang, Chih-Ta Hsieh, Cheng-Ta Chen, Chien-Min Chang, Chih-Ju Division of Neurosurgery Department of Surgery Cathay General Hospital Taipei City Taiwan Ph.D. Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University and National Health Research Institutes Taipei 110 Taiwan Department of Biomedical Engineering Yuanpei University of Medical Technology Hsinchu Taiwan Department of Medicine School of Medicine Fu Jen Catholic University New Taipei City Taiwan School of Medicine National Tsing Hua University Hsinchu Taiwan Division of Neurosurgery Department of Surgery Changhua Christian Hospital Changhua Taiwan Department of Leisure Industry Management National Chin-Yi University of Technology Taichung Taiwan Department of Mechanical Engineering National Central University Taoyuan City Taiwan

Objective: The study aimed to determine the incidence and risk factors associated with bone cement dislodgement in patients with osteoporotic vertebral compression fracture following balloon kyphoplasty treatment. Methods: A retrospective study was conducted on 203 patients who underwent kyphoplasty in 255 vertebral bodies between January 2017 and December 2021. The patients were categorized into two groups: the bone cement dislodgment group (n = 16) and the non-bone cement dislodgement group (n = 239). Various patient characteristics and radiologic parameters were evaluated. Statistical analysis involved the assessment of the background homogeneity of the group by using independent sample t tests, chi-square tests, and Fisher's exact. Univariate and multivariate logistic regression analyses were performed to explore the impact of background variables on cement dislodgement. Results: The results revealed that split-type fracture (χ² = 31.706, p < 0.001), DISH (χ² = 18.827, p = 0.011), pedicle fracture (χ² = 22.246, p < 0.001), endplate deficit (χ² = 14.023, p < 0.001), posterior wall injury (χ² = 29.124, p < 0.001), and intervertebral vacuum cleft (χ² = 21.469, p < 0.001) were the factors that significantly differed between the two groups. The multivariate logistic regression analysis revealed posterior wall injury (OR = 12.983, p = 0.025) and intervertebral vacuum cleft (OR = 5.062, p = 0.024) to be independent risk factors. Conclusion: The incidence of bone cement dislodgement in our study was 6.3%. This study underscores the importance of using preoperative radiologic parameters to predict the risk of bone cement dislodgement following balloon kyphoplasty. © 2024 Elsevier Masson SAS

关键词： Balloon kyphoplasty Bone cement dislodgment Osteoporotic vertebral compression fracture

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Implementing Trust in Non-Small Cell Lung Cancer Diagnosis with a Conformalized Uncertainty-Aware AI Framework in Whole-Slide Images

arXiv

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arXiv 2024年

作者： Zhang, Xiaoge Wang, Tao Yan, Chao Najdawi, Fedaa Zhou, Kai Ma, Yuan Cheung, Yiu-Ming Malin, Bradley A. Department of Industrial and Systems Engineering The Hong Kong Polytechnic University Kowloon Hong Kong Department of Biomedical Informatics Vanderbilt University Medical Center NashvilleTN United States Department of Pathology Microbiology and Immunology Vanderbilt University Medical Center NashvilleTN United States Department of Computing The Hong Kong Polytechnic University Kowloon Hong Kong Department of Mechanical Engineering Research Institute for Intelligent Wearable Systems The Hong Kong Polytechnic University Kowloon Hong Kong Department of Computer Science Hong Kong Baptist University Kowloon Tong Kowloon Hong Kong Department of Computer Science Vanderbilt University NashvilleTN United States Department of Biostatistics Vanderbilt University Medical Center NashvilleTN United States

Ensuring trustworthiness is fundamental to the development of artificial intelligence (AI) that is considered societally responsible, particularly in cancer diagnostics, where a misdiagnosis can have dire consequences. Current digital pathology AI models lack systematic solutions to address trustworthiness concerns arising from model limitations and data discrepancies between model deployment and development environments. To address this issue, we developed TRUECAM, a framework designed to ensure both data and model trustworthiness in non-small cell lung cancer subtyping with whole-slide images. TRUECAM integrates 1) a spectral-normalized neural Gaussian process for identifying out-of-scope inputs and 2) an ambiguity-guided elimination of tiles to filter out highly ambiguous regions, addressing data trustworthiness, as well as 3) conformal prediction to ensure controlled error rates. We systematically evaluated the framework across multiple large-scale cancer datasets, leveraging both task-specific and foundation models, illustrate that an AI model wrapped with TRUECAM significantly outperforms models that lack such guidance, in terms of classification accuracy, robustness, interpretability, and data efficiency, while also achieving improvements in fairness. These findings highlight TRUECAM as a versatile wrapper framework for digital pathology AI models with diverse architectural designs, promoting their responsible and effective applications in real-world settings. © 2024, CC BY.

关键词： Lung cancer

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Sorting of cells with flow channel: Movement of flowing myoblast cell at oblique micro grooves 23

Sorting of cells with flow channel: Movement of flowing myob...

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23rd World Multi-Conference on Systemics, Cybernetics and Informatics, WMSCI 2019

作者： Hashimoto, Shigehiro Hayasaka, Akira Endo, Yuji Biomedical Engineering Department of Mechanical Engineering Kogakuin University Tokyo163-8677 Japan

ISBN: (纸本)9781950492206

The movement of a flowing cell near the oblique micro groove on the bottom surface in the micro flow channel has been measured to sort biological cells in vitro. The micro groove of the rectangular shape (4.5 μm depth, and 0.2 mm length) has been fabricated on the polydimethylsiloxane (PDMS) disk by the photolithography technique. The angle between the flow direction and the longitudinal axis of the groove is 45 degree. Variation has been made on the width (0.03 mm © WMSCI 2019 - 23rd World Multi-Conference on Systemics, Cybernetics and Informatics, Proceedings. All rights reserved.

关键词： Polydimethylsiloxane

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SeqMapPDB: A Standalone Pipeline to Identify Representative Structures of Protein Sequences and Mapping Residue Indices in Real-Time at Proteome Scale

arXiv

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arXiv 2022年

作者： Wang, Boshen Lei, Xue Tian, Wei Perez-Rathke, Alan Liang, Jie Tseng, Yan-Yuan Boinformatics Program Center for Bioinformatics and Quntitative Biology Richard and Loan Hill Department of Biomedical Engineering University of Illinois at Chicago Chicago60612 United States DMolecular Medicine and Genetics Wayne State University Detroit48201 United States

Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale. However, there are technical difficulties in identifying the representative structure of a given protein sequence and providing accurate mapping of residue indices. Existing databases of mapping between structures and sequences are usually static that are not suitable for studying proteomes with frequent gene model revisions. They often do not provide reliable and consistent representative structures that maximizes sequence coverage. Furthermore, proteins isomers are usually not properly resolved. Results: To overcome these difficulties, we have developed a computational pipeline called SeqMapPDB to provide high-quality representative PDB structures of given sequences. It provides mapping to structures that fully cover the sequences when available, or to the set of partial non-overlapping structural domains that maximally cover the query sequence. The residue indices are accurate mapped and isomeric proteins are resolved. SeqMapPDB is efficient and can rapidly carry out proteome-wide mapping to the selected version of reference genomes in real-time. Furthermore, SeqMapPDB provides the flexibility of a stand-alone pipeline for large scale mapping of in-house sequence and structure data. Availability: Our method is available at https://***/lianglabuic/seqmappdb with GNU GPL license. © 2022, CC BY.

关键词： Proteins

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High-flux and stable thin-film evaporation from fiber membranes with interconnected pores

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Joule 2025年

作者： Tianshi Feng Yu Pei Haowen Zhang Brooklyn Asai Gaoweiang Dong Atharva Joshi Abhishek Saha Shengqiang Cai Renkun Chen Department of Mechanical and Aerospace Engineering University of California San Diego La Jolla CA USA Program in Materials Science and Engineering University of California San Diego La Jolla CA USA

Capillary-driven thin-film evaporation in nanoporous membranes has emerged as a promising thermal management strategy for high-power electronic devices, owing to its high theoretical critical heat flux (CHF) enabled by the extensive evaporating areas within the nanopores. In this study, we investigate fiber membranes with three-dimensional interconnected open pores as efficient evaporators. Unlike traditional membranes with isolated pores, these open structures facilitate rapid and uniform liquid transport through multiple pathways, effectively reducing clogging and ensuring consistent wetting across the surface. Capillary-driven evaporation achieved a maximum CHF of over 800 W cm −2 on a relatively large heating area of approximately 0.5 cm 2 , attributed to the larger effective thin-film evaporation areas provided by the open-pore structures. Moreover, the fiber membranes demonstrated long-term stability. These findings suggest that 3D fiber membrane evaporators are highly promising for advanced thermal management, offering efficient, stable cooling solutions to meet the demands of modern electronic systems.

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